[Bioperl-l] test failures in main trunk

[Chris Fields]

Interesting, will look into those.  The first one is troubling (that's  
set up to skip for Algoritm::Diff), the others should be a bit more  
straightforward.

Will have to see why List::MoreUtils is being used, but if it's  
necessary it's an additional dep.

chris

On Sep 18, 2009, at 9:11 AM, Scott Cain wrote:

> With Chris trying to get a release out, I wanted to report these  
> test failures from a fairly virgin system Ubuntu server 8.04.
>
> Scott
>
>
>
> t/SeqIO/raw.t ................................ 1/24 Can't locate  
> Algorithm/Diff.pm in @INC (@INC contains: t/lib . /home/gmod/bioperl- 
> live/blib/lib /home/gmod/bioperl-live/blib/arch /home/gmod/bioperl- 
> live /etc/perl /usr/local/lib/perl/5.8.8 /usr/local/share/perl/ 
> 5.8.8 /usr/lib/perl5 /usr/share/perl5 /usr/lib/perl/5.8 /usr/share/ 
> perl/5.8 /usr/local/lib/site_perl) at t/SeqIO/raw.t line 72.
> BEGIN failed--compilation aborted at t/SeqIO/raw.t line 72.
> # Looks like you planned 24 tests but ran 1.
> # Looks like your test exited with 2 just after 1.
> t/SeqIO/raw.t ................................ Dubious, test  
> returned 2 (wstat 512, 0x200)
>
> t/SeqTools/Backtranslate.t ................... Can't locate ok.pm in  
> @INC (@INC contains: t/lib /home/gmod/bioperl-live/blib/lib /home/ 
> gmod/bioperl-live/blib/arch /home/gmod/bioperl-live /etc/perl /usr/ 
> local/lib/perl/5.8.8 /usr/local/share/perl/5.8.8 /usr/lib/perl5 /usr/ 
> share/perl5 /usr/lib/perl/5.8 /usr/share/perl/5.8 /usr/local/lib/ 
> site_perl .) at t/SeqTools/Backtranslate.t line 9.
> BEGIN failed--compilation aborted at t/SeqTools/Backtranslate.t line  
> 9.
> # Looks like your test exited with 2 before it could output anything.
> t/SeqTools/Backtranslate.t ................... Dubious, test  
> returned 2 (wstat 512, 0x200)
> Failed 8/8 subtests
>
> t/SeqTools/SeqPattern.t ...................... 1/28
> #   Failed test 'use Bio::Tools::SeqPattern;'
> #   at t/SeqTools/SeqPattern.t line 12.
> #     Tried to use 'Bio::Tools::SeqPattern'.
> #     Error:  Can't locate List/MoreUtils.pm in @INC (@INC contains:  
> t/lib . /home/gmod/bioperl-live/blib/lib /home/gmod/bioperl-live/ 
> blib/arch /home/gmod/bioperl-live /etc/perl /usr/local/lib/perl/ 
> 5.8.8 /usr/local/share/perl/5.8.8 /usr/lib/perl5 /usr/share/perl5 / 
> usr/lib/perl/5.8 /usr/share/perl/5.8 /usr/local/lib/site_perl) at  
> Bio/Tools/SeqPattern/Backtranslate.pm line 22.
> # BEGIN failed--compilation aborted at Bio/Tools/SeqPattern/ 
> Backtranslate.pm line 22.
> # Compilation failed in require at Bio/Tools/SeqPattern.pm line 212.
> # Compilation failed in require at (eval 17) line 2.
> # BEGIN failed--compilation aborted at (eval 17) line 2.
> Use of uninitialized value in concatenation (.) or string at Bio/ 
> Tools/SeqPattern.pm line 431.
> Use of uninitialized value in concatenation (.) or string at Bio/ 
> Tools/SeqPattern.pm line 432.
>
> #   Failed test at t/SeqTools/SeqPattern.t line 25.
> #          got: '(CT).{1,80}(C[[]]CT).(AGGGG){1,200}'
> #     expected: '(CT).{1,80}(C[GA][GA]CT).(AGGGG){1,200}'
> Use of uninitialized value in concatenation (.) or string at Bio/ 
> Tools/SeqPattern.pm line 431.
> Use of uninitialized value in concatenation (.) or string at Bio/ 
> Tools/SeqPattern.pm line 432.
>
> #   Failed test at t/SeqTools/SeqPattern.t line 31.
> #          got: '(CT).(C[][]CT){1,80}.(AGGGG){1,200}'
> #     expected: '(CT).(C[AG][AG]CT){1,80}.(AGGGG){1,200}'
> Use of uninitialized value in concatenation (.) or string at Bio/ 
> Tools/SeqPattern.pm line 371.
> Use of uninitialized value in concatenation (.) or string at Bio/ 
> Tools/SeqPattern.pm line 372.
>
> #   Failed test at t/SeqTools/SeqPattern.t line 38.
> #          got: 'A[][]H'
> #     expected: 'A[EQ][DN]H'
> "_reverse_translate_motif" is not exported by the  
> Bio::Tools::SeqPattern::Backtranslate module
> Can't continue after import errors at Bio/Tools/SeqPattern.pm line 539
> # Looks like you planned 28 tests but ran 9.
> # Looks like you failed 4 tests of 9 run.
> # Looks like your test exited with 255 just after 9.
> t/SeqTools/SeqPattern.t ...................... Dubious, test  
> returned 255 (wstat 65280, 0xff00)
> Failed 23/28 subtests
>
>
> -----------------------------------------------------------------------
> Scott Cain, Ph. D. scott at scottcain dot net
> GMOD Coordinator (http://gmod.org/) 216-392-3087
> Ontario Institute for Cancer Research
>
>
>
>
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